A two-step process combining the (equilibrium) glucose isomerization to fructose with selective dehydration of fructose in the obtained sugar mixture to 5-hydroxymethylfurfural (HMF), where glucose is largely unconverted and recycled, represents an attractive concept to increase the overall efficiency for HMF synthesis. This work presents experimental and modelling studies on the conversion of such fructose-glucose mixture to HMF using the sulfuric acid catalyst in a water-methyl isobutyl ketone biphasic system under a wide range of conditions (e.g., temperature, catalyst and sugar concentrations). Through detailed product analyses and ESI-MS spectroscopy, the excess formation of formic acid (together with humins) by the direct sugar/HMF degradation was confirmed and included in the reaction network (neglected in most literatures). The kinetic modelling based on batch experiments in monophasic water well describes the measurements thereof, whereas distinct deviations were found in the prediction of typical literature kinetic models. The incorporation of HMF equilibrium extraction into the developed kinetic model, with consideration of phase volume change as a function of temperature and partial phase miscibility, enables to predict reaction results in the biphasic system in batch. This kinetic model allows to optimize conditions for HMF synthesis that are favored in continuous reactors with minimized back mixing. Based on the model implications, the biphasic system was optimized with slug flow microreactors to better address process intensification and scale-up aspects. Using a simulated fructose-glucose mixture feedstock to represent commercially available high fructose corn syrups, a maximum HMF yield of 81% was obtained at 155 °C over 0.05 M H2SO4 at a residence time of 16 min in the microreactor, with 96% fructose conversion and over 95% of glucose remaining unconverted.